-
Diabetes Nov 2020Metagenome sequencing has not been used in infected bone specimens. This prospective observational study explored the microbiome and its function in patients with...
Metagenome sequencing has not been used in infected bone specimens. This prospective observational study explored the microbiome and its function in patients with diabetic foot osteomyelitis (DFO) and posttraumatic foot osteomyelitis (PFO) based on 16S rRNA sequencing and metagenome sequencing technologies. Spearman analysis was used to explore the correlation between dominant species and clinical indicators of patients with DFO. High-throughput sequencing showed that all the specimens were polymicrobial. The microbial diversity was significantly higher in the DFO group than in the PFO group. , , and were the most abundant microbes in the DFO group. The most abundant microbes in the PFO group were , , and , , and had positive correlation with the duration of diabetic foot infection (DFI_d). was positively correlated with the infection index, while was negatively correlated. The microbial functional genes were more abundant in the DFO group than in the PFO group. Metagenome sequencing is feasible for the analysis of the microbiome in infected bone specimens. Gram-negative bacteria and anaerobes are dominant in DFO.
Topics: Aged; Diabetic Foot; Female; Humans; Male; Metagenome; Metagenomics; Microbiota; Middle Aged; Osteomyelitis; RNA, Bacterial; RNA, Ribosomal, 16S; Sequence Analysis, RNA
PubMed: 32801139
DOI: 10.2337/db20-0503 -
Scientific Reports Apr 2020To construct a saliva-based caries risk assessment model, saliva samples from 176 severe early childhood caries (S-ECC) children and 178 healthy (H) children were...
To construct a saliva-based caries risk assessment model, saliva samples from 176 severe early childhood caries (S-ECC) children and 178 healthy (H) children were screened by real-time PCR-based quantification of the selected species, including Streptococcus mutans, Prevotella pallens, Prevotella denticola and Lactobacillus fermentum. Host factors including caries status, dmft indices, age, gender, and geographic origin were assessed in their influence on abundance of the targeted species, which revealed host caries status as the dominant factor, followed by dmft indices (both P < 0.01). Moreover, levels of S. mutans and P. denticola in the S-ECC group were significantly higher than those in the healthy group (P < 0.001 for S. mutans and P < 0.01 for P. denticola). Interestingly, the co-occurrence network of these targeted species in the S-ECC group differed from that from the healthy group. Finally, based on the combined change pattern of S. mutans and P. pallens, we constructed an S-ECC diagnosis model with an accuracy of 72%. This saliva-based caries diagnosis model is of potential value for circumstances where sampling dental plague is difficult.
Topics: Child; Child, Preschool; Dental Caries; Female; Humans; Limosilactobacillus fermentum; Male; Microbiota; Prevotella; Saliva; Streptococcus mutans
PubMed: 32286402
DOI: 10.1038/s41598-020-63222-1 -
Journal of Dental Sciences Dec 2019
PubMed: 31890133
DOI: 10.1016/j.jds.2019.04.006 -
Annals of the Rheumatic Diseases Jan 2020The causality and pathogenic mechanism of microbiome composition remain elusive in many diseases, including autoimmune diseases such as rheumatoid arthritis (RA). This...
OBJECTIVE
The causality and pathogenic mechanism of microbiome composition remain elusive in many diseases, including autoimmune diseases such as rheumatoid arthritis (RA). This study aimed to elucidate gut microbiome's role in RA pathology by a comprehensive metagenome-wide association study (MWAS).
METHODS
We conducted MWAS of the RA gut microbiome in the Japanese population (=82, =42) by using whole-genome shotgun sequencing of high depth (average 13 Gb per sample). Our MWAS consisted of three major bioinformatic analytic pipelines (phylogenetic analysis, functional gene analysis and pathway analysis).
RESULTS
Phylogenetic case-control association tests showed high abundance of multiple species belonging to the genus (e.g., ) in the RA case metagenome. The non-linear machine learning method efficiently deconvoluted the case-control phylogenetic discrepancy. Gene functional assessments showed that the abundance of one redox reaction-related gene (R6FCZ7) was significantly decreased in the RA metagenome compared with controls. A variety of biological pathways including those related to metabolism (e.g., fatty acid biosynthesis and glycosaminoglycan degradation) were enriched in the case-control comparison. A population-specific link between the metagenome and host genome was identified by comparing biological pathway enrichment between the RA metagenome and the RA genome-wide association study results. No apparent discrepancy in alpha or beta diversities of metagenome was found between RA cases and controls.
CONCLUSION
Our shotgun sequencing-based MWAS highlights a novel link among the gut microbiome, host genome and pathology of RA, which contributes to our understanding of the microbiome's role in RA aetiology.
Topics: Arthritis, Rheumatoid; Bacteroides; Case-Control Studies; Fatty Acids; Female; Gastrointestinal Microbiome; Genome-Wide Association Study; Humans; Japan; Male; Metabolic Networks and Pathways; Metagenome; Metagenomics; Middle Aged; Oxidation-Reduction; Phylogeny; Prevotella; Whole Genome Sequencing
PubMed: 31699813
DOI: 10.1136/annrheumdis-2019-215743